NHMRC Program in Cellular Microbiology

Research output

Research output per year 2016 2017 2018 2019 2020 2021 2023

• 48 Article
• 4 Review Article
• 1 Chapter (Book)
• 1 Other contribution

Research output per year

Research output per year

Search results

• 2023

  The evolutionary mechanism of non-carbapenemase carbapenem-resistant phenotypes in Klebsiella spp

  Rosas, N. C., Wilksch, J., Barber, J., Li, J., Wang, Y., Sun, Z., Rocker, A., Webb, C. T., Perlaza-Jiménez, L., Stubenrauch, C. J., Dhanasekaran, V., Song, J., Taiaroa, G., Davies, M., Strugnell, R. A., Bao, Q., Zhou, T., McDonald, M. J. & Lithgow, T., 6 Jul 2023, In: eLife. 12, 27 p., e83107.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access
• 2022

  A Structurally Characterized Staphylococcus aureus Evolutionary Escape Route from Treatment with the Antibiotic Linezolid

  Perlaza-Jiménez, L., Tan, K. S., Piper, S. J., Johnson, R. M., Bamert, R. S., Stubenrauch, C. J., Wright, A., Lupton, D., Lithgow, T. & Belousoff, M. J., Jul 2022, In: Microbiology Spectrum. 10, 4, 11 p., e0058322.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  2 Citations (Scopus)

• PreAcrs: a machine learning framework for identifying anti-CRISPR proteins

  Zhu, L., Wang, X., Li, F. & Song, J., Dec 2022, In: BMC Bioinformatics. 23, 1, 21 p., 444.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access
  5 Citations (Scopus)

• Tall tails: Cryo-electron microscopy of phage tail DNA ejection conduits

  Hardy, J. M., Dunstan, R. A., Lithgow, T. & Coulibaly, F., Feb 2022, In: Biochemical Society Transactions. 50, 1, p. 459-471 13 p.

  Research output: Contribution to journal › Review Article › Research › peer-review

  Open Access
  5 Citations (Scopus)
• 2021

  Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features

  Zhu, Y-H., Hu, J., Ge, F., Li, F., Song, J., Zhang, Y. & Yu, D-J., 20 May 2021, In: Briefings in Bioinformatics. 22, 3, 14 p., bbaa076.

  Research output: Contribution to journal › Article › Research › peer-review
  12 Citations (Scopus)

• AcrHub: an integrative hub for investigating, predicting and mapping anti-CRISPR proteins

  Wang, J., Dai, W., Li, J., Li, Q., Xie, R., Zhang, Y., Stubenrauch, C. & Lithgow, T., 8 Jan 2021, In: Nucleic Acids Research. 49, D1, p. D630-D638 9 p.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access
  20 Citations (Scopus)

• BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria

  Wang, J., Li, J., Hou, Y., Dai, W., Xie, R., Marquez-Lago, T. T., Leier, A., Zhou, T., Torres, V., Hay, I., Stubenrauch, C., Zhang, Y., Song, J. & Lithgow, T., 8 Jan 2021, In: Nucleic Acids Research. 49, D1, p. D651-D659 9 p.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access
  21 Citations (Scopus)

• Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework

  Li, F., Chen, J., Ge, Z., Wen, Y., Yue, Y., Hayashida, M., Baggag, A., Bensmail, H. & Song, J., 1 Mar 2021, In: Briefings in Bioinformatics. 22, 2, p. 2126-2140 15 p.

  Research output: Contribution to journal › Article › Research › peer-review
  47 Citations (Scopus)

• DeepTorrent: a deep learning-based approach for predicting DNA N4-methylcytosine sites

  Liu, Q., Chen, J., Wang, Y., Li, S., Jia, C., Song, J. & Li, F., 1 Jul 2021, In: Briefings in Bioinformatics. 22, 3, 14 p., bbaa124.

  Research output: Contribution to journal › Article › Research › peer-review
  68 Citations (Scopus)

• DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy

  Xie, R., Li, J., Wang, J., Dai, W., Leier, A., Marquez-Lago, T. T., Akutsu, T., Lithgow, T., Song, J. & Zhang, Y., 20 May 2021, In: Briefings in Bioinformatics. 22, 3, 15 p., bbaa125.

  Research output: Contribution to journal › Article › Research › peer-review
  35 Citations (Scopus)

• Mechanistic Insights into the Capsule-Targeting Depolymerase from a Klebsiella pneumoniae Bacteriophage

  Dunstan, R. A., Bamert, R. S., Belousoff, M. J., Short, F. L., Barlow, C. K., Pickard, D. J., Wilksch, J. J., Schittenhelm, R. B., Strugnell, R. A., Dougan, G. & Lithgow, T., 3 Sept 2021, In: Microbiology Spectrum. 9, 1, 15 p., e01023-21.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access
  19 Citations (Scopus)

• Stepwise evolution of carbapenem-resistance, captured in patient samples and evident in global genomics of Klebsiella pneumoniae

  Perlaza-Jimenez, L., Wilksch, J. J., Stubenrauch, C. J., Chen, T., Zhao, Y., Zhou, T., Lithgow, T. & Dhanasekaran, V., 25 Jun 2021, 28 p. medRxiv.

  Research output: Other contribution › Research

• The Carbapenemase BKC-1 from Klebsiella pneumoniae Is Adapted for Translocation by Both the Tat and Sec Translocons

  Bharathwaj, M., Webb, C. T., Vadlamani, G., Stubenrauch, C. J., Palmer, T. & Lithgow, T., May 2021, In: mBio. 12, 3, 15 p., e0130221.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access
  6 Citations (Scopus)

• Why can deep convolutional neural networks improve protein fold recognition? A visual explanation by interpretation

  Liu, Y., Zhu, Y. H., Song, X., Song, J. & Yu, D. J., Sept 2021, In: Briefings in Bioinformatics. 22, 5, p. 1-14 14 p.

  Research output: Contribution to journal › Article › Research › peer-review
  10 Citations (Scopus)
• 2020

  Characterization of the Core Ribosomal Binding Region for the Oxazolidone Family of Antibiotics Using Cryo-EM

  Wright, A., Deane-Alder, K., Marschall, E., Bamert, R., Venugopal, H., Lithgow, T., Lupton, D. W. & Belousoff, M. J., 12 Jun 2020, In: ACS Pharmacology & Translational Science. 3, 3, p. 425-432 8 p.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  18 Citations (Scopus)

• DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites

  Li, F., Chen, J., Leier, A., Marquez-Lago, T., Liu, Q., Wang, Y., Revote, J., Smith, A. I., Akutsu, T., Webb, G. I., Kurgan, L. & Song, J., 15 Feb 2020, In: Bioinformatics. 36, 4, p. 1057-1065 9 p.

  Research output: Contribution to journal › Article › Research › peer-review
  93 Citations (Scopus)

• Dynamic epidemiology and virulence characteristics of carbapenem-resistant klebsiella pneumoniae in wenzhou, China from 2003 to 2016

  Zhao, Y., Zhang, S., Fang, R., Wu, Q., Li, J., Zhang, Y., Rocker, A., Cao, J., Lithgow, T. & Zhou, T., 31 Mar 2020, In: Infection and Drug Resistance. 13, p. 931-940 10 p.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  8 Citations (Scopus)

• Forensic genomics of a novel klebsiella quasipneumoniae type from a neonatal intensive care unit in China reveals patterns of colonization, evolution and epidemiology

  Perlaza-Jiménez, L., Wu, Q., Torres, V. V. L., Zhang, X., Li, J., Rocker, A., Lithgow, T., Zhou, T. & Vijaykrishna, D., 15 Sept 2020, In: Microbial Genomics. 6, 10, 10 p., 000433.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  8 Citations (Scopus)

• Formation and function of bacterial organelles

  Greening, C. & Lithgow, T., Dec 2020, In: Nature Reviews Microbiology. 18, 12, p. 677-689 13 p.

  Research output: Contribution to journal › Review Article › Research › peer-review
  70 Citations (Scopus)

• Global trends in proteome remodeling of the outer membrane modulate antimicrobial permeability in Klebsiella pneumoniae

  Rocker, A., Lacey, J. A., Belousoff, M. J., Wilksch, J. J., Strugnell, R. A., Davies, M. R. & Lithgow, T., 14 Apr 2020, In: mBio. 11, 2, 16 p., e00603-20.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  28 Citations (Scopus)

• Investigation of LuxS-mediated quorum sensing in Klebsiella pneumoniae

  Chen, L., Wilksch, J. J., Liu, H., Zhang, X., Torres, V. V. L., Bi, W., Mandela, E., Cao, J., Li, J., Lithgow, T. & Zhou, T., 28 Jan 2020, In: Journal of Medical Microbiology. 69, 3, p. 402-413 12 p.

  Research output: Contribution to journal › Article › Research › peer-review
  20 Citations (Scopus)

• Mapping bacterial effector arsenals: in vivo and in silico approaches to defining the protein features dictating effector secretion by bacteria

  Lee, Y. W., Wang, J., Newton, H. J. & Lithgow, T., Oct 2020, In: Current Opinion in Microbiology. 57, p. 13-21 9 p.

  Research output: Contribution to journal › Review Article › Research › peer-review
  7 Citations (Scopus)

• PaCRISPR: a server for predicting and visualizing anti-CRISPR proteins

  Wang, J., Dai, W., Li, J., Xie, R., Dunstan, R. A., Stubenrauch, C., Zhang, Y. & Lithgow, T., 27 May 2020, In: Nucleic Acids Research. 48, W1, p. W348-W357 10 p.

  Research output: Contribution to journal › Article › Research › peer-review
  27 Citations (Scopus)

• PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins

  Zhang, Y., Yu, S., Xie, R., Li, J., Leier, A., Marquez-Lago, T. T., Akutsu, T., Smith, A. I., Ge, Z., Wang, J., Lithgow, T. & Song, J., 1 Feb 2020, In: Bioinformatics. 36, 3, p. 704-712 9 p.

  Research output: Contribution to journal › Article › Research › peer-review
  34 Citations (Scopus)

• The architecture and stabilisation of flagellotropic tailed bacteriophages

  Hardy, J. M., Dunstan, R. A., Grinter, R., Belousoff, M. J., Wang, J., Pickard, D., Venugopal, H., Dougan, G., Lithgow, T. & Coulibaly, F., 27 Jul 2020, In: Nature Communications. 11, 1, 11 p., 3748.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  20 Citations (Scopus)

• The crystal structure of the TonB-dependent transporter YncD reveals a positively charged substrate-binding site

  Grinter, R. & Lithgow, T., 1 May 2020, In: Acta Crystallographica Section D: Structural Biology. 76, p. 484-495 12 p.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  8 Citations (Scopus)
• 2019

  An Outbreak of Carbapenem-Resistant and Hypervirulent Klebsiella pneumoniae in an Intensive Care Unit of a Major Teaching Hospital in Wenzhou, China

  Zhao, Y., Zhang, X., Torres, V. V. L., Liu, H., Rocker, A., Zhang, Y., Wang, J., Chen, L., Bi, W., Lin, J., Strugnell, R. A., Zhang, S., Lithgow, T., Zhou, T. & Cao, J., 19 Aug 2019, In: Frontiers in Public Health. 7, 11 p., 229.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  28 Citations (Scopus)

• Bastion3: A two-layer ensemble predictor of type III secreted effectors

  Wang, J., Li, J., Yang, B., Xie, R., Marquez-Lago, T. T., Leier, A., Hayashida, M., Akutsu, T., Zhang, Y., Chou, K-C., Selkrig, J., Zhou, T., Song, J. & Lithgow, T., 1 Jun 2019, In: Bioinformatics. 35, 12, p. 2017-2028 12 p., bty914.

  Research output: Contribution to journal › Article › Research › peer-review
  55 Citations (Scopus)

• cryoEM-Guided Development of Antibiotics for Drug-Resistant Bacteria

  Belousoff, M. J., Venugopal, H., Wright, A., Seoner, S., Stuart, I., Stubenrauch, C., Bamert, R. S., Lupton, D. W. & Lithgow, T., 5 Mar 2019, In: ChemMedChem. 14, 5, p. 527-231 5 p.

  Research output: Contribution to journal › Article › Research › peer-review
  17 Citations (Scopus)

• Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches

  Wang, J., Yang, B., An, Y., Marquez-Lago, T., Leier, A., Wilksch, J., Hong, Q., Zhang, Y., Hayashida, M., Akutsu, T., Webb, G. I., Strugnell, R. A., Song, J. & Lithgow, T., 21 May 2019, In: Briefings in Bioinformatics. 20, 3, p. 931-951 21 p.

  Research output: Contribution to journal › Article › Research › peer-review
  54 Citations (Scopus)

• The multifunctional enzyme S-adenosylhomocysteine/methylthioadenosine nucleosidase is a key metabolic enzyme in the virulence of Salmonella enterica var Typhimurium

  Husna, A. U., Wang, N., Wilksch, J. J., Newton, H. J., Hocking, D. M., Hay, I. D., Cobbold, S. A., Davies, M. R., McConville, M. J., Lithgow, T. & Strugnell, R. A., 29 Nov 2019, In: Biochemical Journal. 476, 22, p. 3435-3453 19 p.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  2 Citations (Scopus)

• The TAM: A Translocation and Assembly Module of the β-Barrel Assembly Machinery in Bacterial Outer Membranes

  Stubenrauch, C. J. & Lithgow, T., 27 Feb 2019, In: EcoSal Plus. 8, 2, p. 1-7 7 p.

  Research output: Contribution to journal › Article › Research › peer-review
  19 Citations (Scopus)

• The TAM: A translocation and assembly module of the β-barrel assembly machinery in bacterial outer membranes

  Stubenrauch, C. J. & Lithgow, T., 1 Jan 2019, Protein Secretion in Bacteria. Sandkvist, M., Cascales, E. & Christie, P. J. (eds.). Washington, DC, USA: Wiley-Academy, p. 103-111 9 p.

  Research output: Chapter in Book/Report/Conference proceeding › Chapter (Book) › Other › peer-review

• Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods

  Li, F., Wang, Y., Li, C., Marquez-Lago, T. T., Leier, A., Rawlings, N. D., Haffari, G., Revote, J., Akutsu, T., Chou, K-C., Purcell, A. W., Pike, R. N., Webb, G. I., Smith, A. I., Lithgow, T., Daly, R. J., Whisstock, J. C. & Song, J., 27 Nov 2019, In: Briefings in Bioinformatics. 20, 6, p. 2150-2166 17 p.

  Research output: Contribution to journal › Article › Research › peer-review
  63 Citations (Scopus)
• 2018

  An investigation into the Omp85 protein BamK in hypervirulent Klebsiella pneumoniae, and its role in outer membrane biogenesis

  Torres, V. V. L., Heinz, E., Stubenrauch, C. J., Wilksch, J. J., Cao, H., Yang, J., Clements, A., Dunstan, R. A., Alcock, F., Webb, C. T., Dougan, G., Strugnell, R. A., Hay, I. D. & Lithgow, T., Sept 2018, In: Molecular Microbiology. 109, 5, p. 584-599 16 p.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  5 Citations (Scopus)

• Bastion6: A bioinformatics approach for accurate prediction of type VI secreted effectors

  Wang, J., Yang, B., Leier, A., Marquez-Lago, T., Hayashida, M., Rocker, A., Zhang, Y., Akutsu, T., Chou, K-C., Strugnell, R. A., Song, J. & Lithgow, T., 1 Jan 2018, In: Bioinformatics. 34, 15, p. 2546-2555 10 p.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  84 Citations (Scopus)

• Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI

  An, Y., Wang, J., Li, C., Leier, A., Marquez-Lago, T., Wilksch, J., Zhang, Y., Webb, G. I., Song, J. & Lithgow, T., 1 Jan 2018, In: Briefings in Bioinformatics. 19, 1, p. 148-161 14 p., bbw100.

  Research output: Contribution to journal › Article › Research › peer-review
  48 Citations (Scopus)

• FusC, a member of the M16 protease family acquired by bacteria for iron piracy against plants

  Grinter, R., Hay, I. D., Song, J., Wang, J., Teng, D., Dhanesakaran, V., Wilksch, J. J., Davies, M. R., Littler, D., Beckham, S. A., Henderson, I. R., Strugnell, R. A., Dougan, G. & Lithgow, T., 2 Aug 2018, In: PLoS Biology. 16, 8, 21 p., e2006026.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  11 Citations (Scopus)

• Structure and membrane topography of the vibrio-type secretin complex from the type 2 secretion system of enteropathogenic Escherichia coli

  Hay, I. D., Belousoff, M. J., Dunstan, R. A., Bamert, R. S. & Lithgow, T., 1 Mar 2018, In: Journal of Bacteriology. 200, 5, 15 p., e00521-17.

  Research output: Contribution to journal › Article › Research › peer-review
  31 Citations (Scopus)

• The WD40 Protein BamB Mediates Coupling of BAM Complexes into Assembly Precincts in the Bacterial Outer Membrane

  Gunasinghe, S. D., Shiota, T., Stubenrauch, C. J., Schulze, K. E., Webb, C. T., Fulcher, A. J., Dunstan, R. A., Hay, I. D., Naderer, T., Whelan, D. R., Bell, T. D. M., Elgass, K. D., Strugnell, R. A. & Lithgow, T., 29 May 2018, In: Cell Reports. 23, 9, p. 2782-2794 13 p.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  53 Citations (Scopus)
• 2017

  Constraints on lateral gene transfer in promoting fimbrial usher protein diversity and function

  Stubenrauch, C. J., Dougan, G., Lithgow, T. & Heinz, E., 15 Nov 2017, In: Open Biology. 7, 11, 10 p., 170144.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  9 Citations (Scopus)

• Extensively drug-resistant klebsiella pneumoniae causing nosocomial bloodstream infections in China: Molecular investigation of antibiotic resistance determinants, Informing therapy, and clinical outcomes

  Bi, W., Liu, H., Dunstan, R. A., Li, B., Torres, V. V. L., Cao, J., Chen, L., Wilksch, J. J., Strugnell, R. A., Lithgow, T. & Zhou, T., 30 Jun 2017, In: Frontiers in Microbiology. 8, 12 p., 1230.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  47 Citations (Scopus)

• Knowledge-Transfer learning for prediction of matrix metalloprotease substrate-cleavage sites

  Wang, Y., Song, J., Marquez-Lago, T., Leier, A., Li, C., Lithgow, T., Webb, G. I. & Shen, H-B., 1 Dec 2017, In: Scientific Reports. 7, 1, 5755.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  17 Citations (Scopus)

• Phylogenetic analysis of Klebsiella pneumoniae from hospitalized children, Pakistan

  Ejaz, H., Wang, N., Wilksch, J. J., Page, A. J., Cao, H., Gujaran, S., Keane, J. A., Lithgow, T., Ul-Haq, I., Dougan, G., Strugnell, R. A. & Heinz, E., 1 Nov 2017, In: Emerging Infectious Diseases. 23, 11, p. 1872-1875 4 p.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  33 Citations (Scopus)

• POSSUM: A bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles

  Wang, J., Yang, B., Revote, J., Leier, A., Marquez-Lago, T. T., Webb, G., Song, J., Chou, K-C. & Lithgow, T., 1 Jan 2017, In: Bioinformatics. 33, 17, p. 2756-2758 3 p.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  126 Citations (Scopus)

• Reductive evolution in outer membrane protein biogenesis has not compromised cell surface complexity in Helicobacter pylori

  Webb, C. T., Chandrapala, D., Oslan, S. N., Bamert, R. S., Grinter, R. D., Dunstan, R. A., Gorrell, R. J., Song, J., Strugnell, R. A., Lithgow, T. & Kwok, T., 1 Dec 2017, In: MicrobiologyOpen. 6, 6, 17 p., e00513.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  6 Citations (Scopus)

• SecretEPDB: A comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems

  An, Y., Wang, J., Li, C., Revote, J., Zhang, Y., Naderer, T., Hayashida, M., Akutsu, T., Webb, G. I., Lithgow, T. & Song, J., 23 Jan 2017, In: Scientific Reports. 7, 10 p., 41031.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  33 Citations (Scopus)

• Structural basis for linezolid binding site rearrangement in the Staphylococcus aureus ribosome

  Belousoff, M. J., Eyal, Z., Radjainia, M., Ahmed, T., Bamert, R. S., Matzov, D., Bashan, A., Zimmerman, E., Mishra, S., Cameron, D., Elmlund, H., Peleg, A. Y., Bhushan, S., Lithgow, T. & Yonath, A., 9 May 2017, In: mBio. 8, 3, 7 p., e00395-17.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  32 Citations (Scopus)

• Structural basis for substrate selection by the translocation and assembly module of the β-barrel assembly machinery

  Bamert, R. S., Lundquist, K., Hwang, H., Webb, C. T., Shiota, T., Stubenrauch, C. J., Belousoff, M. J., Goode, R. J. A., Schittenhelm, R. B., Zimmerman, R., Jung, M., Gumbart, J. C. & Lithgow, T., 1 Oct 2017, In: Molecular Microbiology. 106, 1, p. 142-156 15 p.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  26 Citations (Scopus)

• Structural basis of type 2 secretion system engagement between the inner and outer bacterial membranes

  Hay, I. D., Belousoff, M. J. & Lithgow, T., 17 Oct 2017, In: mBio. 8, 5, 6 p., e01344-17.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  36 Citations (Scopus)